PDX3 (YBR035C, P38075) notes

Identity

Pyridoxamine 5'-phosphate oxidase (PNPOx), EC 1.4.3.5, FMN-dependent; PNPOx family with both PF01243 (PNPOx_N) and PF10590 (PNP_phzG_C) domains; crystal structure 1CI0 (homodimer with 2 FMN) [UniProt:P38075].
Paralog-like YLR456W and YPR172W carry only PF01243 and are NOT PNP/PMP oxidases PMID:26327315 -- relevant to the module: only Pdx3 is the yeast PNPOx.

Original genetic/biochemical identification: aux30 (pdx3) mutants lack P(N/M)P oxidase activity and cannot use pyridoxine, but grow on pyridoxal or pyridoxamine PMID:7896706. Pleiotropic phenotypes (heme/sterol uptake) are downstream of PLP shortage.
Recombinant Pdx3 binds FMN and oxidises PNP to PLP [PMID:26327315 "On the other hand, Pdx3 recombinant protein exhibits all expected properties of a bona fide P(N/M)P oxidase."; "Note that purified Pdx3 presents the characteristic yellow color of proteins that are bound to FMN."].

Found in the mitochondrial intermembrane space proteome (Bax-release SILAC) PMID:22984289; previous localization "Unknown" in that table. Whether there is also a cytosolic pool is not established.

Yeast makes PLP de novo via Snz1/Sno1 (directly), so Pdx3 functions in salvage (PNP/PMP -> PLP), downstream of the kinase Bud16. InterPro2GO "pyridoxine biosynthetic process" reflects bacterial PdxH context and is not appropriate here.

Status set to COMPLETE. All summaries were left verbatim (the PTHR10851
family review quotes two of them); reason added to every row that lacked
one, and the PAINT IBD rows are now quoted from
interpro/panther/PTHR10851/PTHR10851-paint.tsv on the three IBA rows.
Cytosol (RCA, YeastPathways default compartment) resolved from UNDECIDED to
MARK_AS_OVER_ANNOTATED: the only localization assay places Pdx3 in the IMS,
and the IMS proteome paper notes PMID:22984289. A
cytosolic pool stays an open question (suggested_questions).
Mitochondrion IBA kept (ACCEPT) after the organelle-policy check: the node is
seeded by Pdx3 itself and the IMS proteome supports the organelle claim.
GO:0042823 IBA kept ACCEPT as the family-level process; the yeast-specific
route is GO:0009443 salvage. FMN binding ACCEPT, matching the bacterial PdxH
reviews completed in the same batch.